Pagoo - Publication Scripts

Scripts supporting pagoo's publication.

Description

This repo contains 2 scripts to reproduce the analyses described in the pagoo manuscript. timing_benchmark.R runs roary and evaluates timings over a set of pagoo's operations. Cfetus_pangenome_example.R downloads a Campylobacter fetus dataset and uses pagoo along with other R packages to perform a series of analyses.

Data

Data required by timing_benchmark.R is hosted at: https://zenodo.org/record/3341535#.YA7_8ZqvHJE (Publication: Decano & Downing, 2019, dataset doi:10.5281/zenodo.3341534). The script automatically downloads and decompress it in the working directory.

Data required by Cfetus_pangenome_example.R is hosted at: https://figshare.com/articles/dataset/Campylobacter_fetus_genomes_and_pangenome_for_pagoo_demo/13622354 . The script automatically downloads and decompress it in the working directory.

Singularity container

This repo also contains a Singularity file to build a Singularity image with all dependencies needed to run the scripts.

Build

To manually build the container:

git clone https://github.com/iferres/pagoo_publication_scripts
cd ./pagoo_publication_scripts
sudo singularity build pagoo_publicaction_container.sif Singularity

Pull

To pull the prebuilt container hosted at singularity-hub:

singularity pull pagoo_publication_container.sif shub://iferres/pagoo_publication_scripts

Run

To run the C. fetus script, all at once:

# The following expects the script (.R) and the container (.sif) 
# in the current working directory.
singularity exec pagoo_publication_container.sif Rscript --vanilla Cfetus_pangenome_example.R

If you want to play more freely with the package, you can shell into the container, start an interactive R session, and load pagoo:

# Start container
singularity shell pagoo_publication_container.sif
# Start R
R

# Inside R, load pagoo
library(pagoo)

Known limitations

Shiny app doesn't work from within the container, although it is not needed by the scripts.